Continuity mistake: When Thade takes the weapon from Leo the weapon is a futuristic laser type gun. When Thade is firing the weapon after being locked in the command centre, the gun is a stainless steel Beretta brigadier model. (01:50:00)
Revealing mistake: After the trained chimp is shot and is crawling into the cage, they show a shot of an ape turning around. You don't even have to look hard to see it but there's a two inch strip all the way down his face with no makeup. Clear as day. (01:41:30)
Answer: To prevent anyone else from learning that Leo came from space. After Pericles' ship crashed, there was a prophecy of a second coming of Semos, the founder of Ape civilization. Thade wants to kill all humans, so if anyone found out, it would be considered a sign and the council might consider making peace with the humans.
Captain Defenestrator